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TitleA 2-Tyr-1-carboxylate Mononuclear Iron Center Forms the Active Site of a Paracoccus Dimethylformamidase.
Journal, issue, pagesAngew Chem Int Ed Engl, Vol. 59, Issue 39, Page 16961-16966, Year 2020
Publish dateSep 21, 2020
AuthorsChetan Kumar Arya / Swati Yadav / Jonathan Fine / Ana Casanal / Gaurav Chopra / Gurunath Ramanathan / Kutti R Vinothkumar / Ramaswamy Subramanian /
PubMed AbstractN,N-dimethyl formamide (DMF) is an extensively used organic solvent but is also a potent pollutant. Certain bacterial species from genera such as Paracoccus, Pseudomonas, and Alcaligenes have evolved ...N,N-dimethyl formamide (DMF) is an extensively used organic solvent but is also a potent pollutant. Certain bacterial species from genera such as Paracoccus, Pseudomonas, and Alcaligenes have evolved to use DMF as a sole carbon and nitrogen source for growth via degradation by a dimethylformamidase (DMFase). We show that DMFase from Paracoccus sp. strain DMF is a halophilic and thermostable enzyme comprising a multimeric complex of the α β or (α β ) type. One of the three domains of the large subunit and the small subunit are hitherto undescribed protein folds of unknown evolutionary origin. The active site consists of a mononuclear iron coordinated by two Tyr side-chain phenolates and one carboxylate from Glu. The Fe ion in the active site catalyzes the hydrolytic cleavage of the amide bond in DMF. Kinetic characterization reveals that the enzyme shows cooperativity between subunits, and mutagenesis and structural data provide clues to the catalytic mechanism.
External linksAngew Chem Int Ed Engl / PubMed:32452120 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution2.8 - 3.2 Å
Structure data

0988

6lvb

EMDB-0988, PDB-6lvb:
Structure of Dimethylformamidase, tetramer
Method: EM (single particle) / Resolution: 2.8 Å

0989

6lvc

EMDB-0989, PDB-6lvc:
Structure of Dimethylformamidase, dimer
Method: EM (single particle) / Resolution: 3.0 Å

0990

6lvd

EMDB-0990, PDB-6lvd:
Structure of Dimethylformamidase, tetramer, Y440A mutant
Method: EM (single particle) / Resolution: 3.2 Å

0991

6lve

EMDB-0991, PDB-6lve:
Structure of Dimethylformamidase, tetramer, E521A mutant
Method: EM (single particle) / Resolution: 3.1 Å

PDB-6lvv:
N, N-dimethylformamidase
Method: X-RAY DIFFRACTION / Resolution: 2.8 Å

Chemicals

ChemComp-FE:
Unknown entry / Iron

ChemComp-HOH:
WATER / Water

ChemComp-EDO:
1,2-ETHANEDIOL / Ethylene glycol

Source
  • paracoccus sp. ssg05 (bacteria)
KeywordsHYDROLASE / ab polypeptide / mononuclear iron / amidohydrolase / tetramer / Amidase / Linear aliphatic amidohydrolase / metallo-amidase / heterotetramer.

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